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Results: 1 to 20 of 110

1.

PANGEA: pipeline for analysis of next generation amplicons.

Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.

ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25.

PMID:
20182525
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.

PMID:
23184592
[PubMed - indexed for MEDLINE]
3.

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows.

Barriuso J, Valverde JR, Mellado RP.

BMC Bioinformatics. 2011 Dec 14;12:473. doi: 10.1186/1471-2105-12-473.

PMID:
22168258
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

PMID:
21460107
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries.

Yu Y, Breitbart M, McNairnie P, Rohwer F.

BMC Bioinformatics. 2006 Feb 7;7:57.

PMID:
16464253
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Rethinking microbial diversity analysis in the high throughput sequencing era.

Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF.

J Microbiol Methods. 2011 Jul;86(1):42-51. doi: 10.1016/j.mimet.2011.03.014. Epub 2011 Mar 30.

PMID:
21457733
[PubMed - indexed for MEDLINE]
Free Article
7.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.

Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD.

BMC Microbiol. 2010 Jul 30;10:206. doi: 10.1186/1471-2180-10-206.

PMID:
20673359
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data.

Sun Y, Cai Y, Mai V, Farmerie W, Yu F, Li J, Goodison S.

Nucleic Acids Res. 2010 Dec;38(22):e205. doi: 10.1093/nar/gkq872. Epub 2010 Oct 6.

PMID:
20929878
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons.

Shepherd ML, Swecker WS Jr, Jensen RV, Ponder MA.

FEMS Microbiol Lett. 2012 Jan;326(1):62-8. doi: 10.1111/j.1574-6968.2011.02434.x. Epub 2011 Nov 2.

PMID:
22092776
[PubMed - indexed for MEDLINE]
Free Article
10.

Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning.

Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR.

Appl Environ Microbiol. 1999 Apr;65(4):1662-9.

PMID:
10103265
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Low sequencing efforts bias analyses of shared taxa in microbial communities.

Lemos LN, Fulthorpe RR, Roesch LF.

Folia Microbiol (Praha). 2012 Sep;57(5):409-13. doi: 10.1007/s12223-012-0155-0. Epub 2012 May 5.

PMID:
22562492
[PubMed - indexed for MEDLINE]
12.

Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes.

Duarte GF, Rosado AS, Seldin L, de Araujo W, van Elsas JD.

Appl Environ Microbiol. 2001 Mar;67(3):1052-62.

PMID:
11229891
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Analysis of mixed sequencing chromatograms and its application in direct 16S rRNA gene sequencing of polymicrobial samples.

Kommedal O, Karlsen B, Saebø O.

J Clin Microbiol. 2008 Nov;46(11):3766-71. doi: 10.1128/JCM.00213-08. Epub 2008 Sep 3.

PMID:
18768654
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.

PMID:
20534432
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis.

Dunbar J, Ticknor LO, Kuske CR.

Appl Environ Microbiol. 2000 Jul;66(7):2943-50.

PMID:
10877790
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A gzip-based algorithm to identify bacterial families by 16S rRNA.

Santoni D, Romano-Spica V.

Lett Appl Microbiol. 2006 Apr;42(4):312-4.

PMID:
16599980
[PubMed - indexed for MEDLINE]
17.

Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park.

Hamamura N, Olson SH, Ward DM, Inskeep WP.

Appl Environ Microbiol. 2005 Oct;71(10):5943-50.

PMID:
16204508
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Influence of soil characteristics on the diversity of bacteria in the Southern Brazilian Atlantic Forest.

Faoro H, Alves AC, Souza EM, Rigo LU, Cruz LM, Al-Janabi SM, Monteiro RA, Baura VA, Pedrosa FO.

Appl Environ Microbiol. 2010 Jul;76(14):4744-9. doi: 10.1128/AEM.03025-09. Epub 2010 May 21.

PMID:
20495051
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.

Hur I, Chun J.

J Microbiol. 2004 Mar;42(1):9-13.

PMID:
15357285
[PubMed - indexed for MEDLINE]
Free Article
20.

FastGroup: a program to dereplicate libraries of 16S rDNA sequences.

Seguritan V, Rohwer F.

BMC Bioinformatics. 2001;2:9. Epub 2001 Oct 16.

PMID:
11707150
[PubMed - indexed for MEDLINE]
Free PMC Article
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